Starting phenix.real_space_refine on Mon Mar 11 12:17:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/03_2024/8hii_34817.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/03_2024/8hii_34817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/03_2024/8hii_34817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/03_2024/8hii_34817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/03_2024/8hii_34817.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hii_34817/03_2024/8hii_34817.pdb" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 5284 2.51 5 N 1372 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 145": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "N ARG 27": "NH1" <-> "NH2" Residue "N TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 25": "NH1" <-> "NH2" Residue "L ARG 213": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8212 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3969 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 17, 'TRANS': 480} Chain breaks: 1 Chain: "H" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1632 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Time building chain proxies: 4.81, per 1000 atoms: 0.59 Number of scatterers: 8212 At special positions: 0 Unit cell: (66.34, 101.65, 150.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1530 8.00 N 1372 7.00 C 5284 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 40.8% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid -80 through -64 Processing helix chain 'A' and resid -58 through -43 removed outlier: 3.785A pdb=" N ALA A -54 " --> pdb=" O GLN A -58 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A -43 " --> pdb=" O ALA A -47 " (cutoff:3.500A) Processing helix chain 'A' and resid -38 through -33 removed outlier: 4.211A pdb=" N ASP A -33 " --> pdb=" O PRO A -37 " (cutoff:3.500A) Processing helix chain 'A' and resid -25 through -3 removed outlier: 3.805A pdb=" N ARG A -21 " --> pdb=" O MET A -25 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A -5 " --> pdb=" O ASP A -9 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN A -3 " --> pdb=" O LEU A -7 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 18 Processing helix chain 'A' and resid 27 through 39 removed outlier: 3.793A pdb=" N LEU A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET A 38 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 60 through 67 Processing helix chain 'A' and resid 67 through 90 removed outlier: 3.828A pdb=" N VAL A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 4.702A pdb=" N LEU A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 Processing helix chain 'A' and resid 115 through 132 removed outlier: 3.755A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.685A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 176 Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.736A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 267 through 296 removed outlier: 4.108A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 Processing helix chain 'A' and resid 333 through 354 removed outlier: 4.657A pdb=" N LEU A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 338 " --> pdb=" O TRP A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.845A pdb=" N ALA A 367 " --> pdb=" O TRP A 363 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 386 Processing helix chain 'A' and resid 392 through 419 Processing helix chain 'A' and resid 427 through 451 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.508A pdb=" N ASP H 93 " --> pdb=" O ARG H 90 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 94' Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.889A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.530A pdb=" N ASP N 90 " --> pdb=" O LYS N 87 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 87 through 91' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.967A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 130 Processing helix chain 'L' and resid 184 through 188 removed outlier: 3.543A pdb=" N ASP L 187 " --> pdb=" O SER L 184 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR L 188 " --> pdb=" O LYS L 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 184 through 188' Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.785A pdb=" N LEU H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR H 53 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.134A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.134A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 165 through 168 removed outlier: 4.237A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.154A pdb=" N THR N 118 " --> pdb=" O GLY N 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.612A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR N 110 " --> pdb=" O ILE N 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.594A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN L 91 " --> pdb=" O THR L 99 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.594A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.679A pdb=" N ASN L 139 " --> pdb=" O SER L 116 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 147 through 148 removed outlier: 3.668A pdb=" N LYS L 147 " --> pdb=" O THR L 199 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 151 through 152 438 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2560 1.34 - 1.46: 2052 1.46 - 1.58: 3763 1.58 - 1.70: 0 1.70 - 1.82: 38 Bond restraints: 8413 Sorted by residual: bond pdb=" C VAL A 81 " pdb=" N PRO A 82 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.97e+00 bond pdb=" C LYS H 215 " pdb=" N PRO H 216 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.32e+00 bond pdb=" CA LYS L 185 " pdb=" C LYS L 185 " ideal model delta sigma weight residual 1.522 1.555 -0.033 1.72e-02 3.38e+03 3.75e+00 bond pdb=" C SER L 8 " pdb=" N PRO L 9 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.38e+00 bond pdb=" C THR A 93 " pdb=" N PRO A 94 " ideal model delta sigma weight residual 1.336 1.355 -0.020 1.25e-02 6.40e+03 2.45e+00 ... (remaining 8408 not shown) Histogram of bond angle deviations from ideal: 100.26 - 107.02: 236 107.02 - 113.77: 4613 113.77 - 120.53: 3320 120.53 - 127.28: 3180 127.28 - 134.03: 95 Bond angle restraints: 11444 Sorted by residual: angle pdb=" N THR A 69 " pdb=" CA THR A 69 " pdb=" C THR A 69 " ideal model delta sigma weight residual 109.81 118.52 -8.71 2.21e+00 2.05e-01 1.55e+01 angle pdb=" C ASN L 212 " pdb=" N ARG L 213 " pdb=" CA ARG L 213 " ideal model delta sigma weight residual 121.70 127.96 -6.26 1.80e+00 3.09e-01 1.21e+01 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C PHE N 103 " pdb=" N TYR N 104 " pdb=" CA TYR N 104 " ideal model delta sigma weight residual 122.46 126.93 -4.47 1.41e+00 5.03e-01 1.01e+01 angle pdb=" CA GLU H 108 " pdb=" C GLU H 108 " pdb=" N PRO H 109 " ideal model delta sigma weight residual 118.44 123.03 -4.59 1.59e+00 3.96e-01 8.33e+00 ... (remaining 11439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.22: 4753 15.22 - 30.44: 149 30.44 - 45.65: 44 45.65 - 60.87: 0 60.87 - 76.09: 11 Dihedral angle restraints: 4957 sinusoidal: 1880 harmonic: 3077 Sorted by residual: dihedral pdb=" CB CYS H 154 " pdb=" SG CYS H 154 " pdb=" SG CYS H 210 " pdb=" CB CYS H 210 " ideal model delta sinusoidal sigma weight residual 93.00 169.09 -76.09 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 156.40 23.60 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ASN A -61 " pdb=" C ASN A -61 " pdb=" N ALA A -60 " pdb=" CA ALA A -60 " ideal model delta harmonic sigma weight residual -180.00 -159.18 -20.82 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 4954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 936 0.049 - 0.097: 283 0.097 - 0.146: 68 0.146 - 0.194: 7 0.194 - 0.243: 2 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA THR A 69 " pdb=" N THR A 69 " pdb=" C THR A 69 " pdb=" CB THR A 69 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE A 134 " pdb=" CA ILE A 134 " pdb=" CG1 ILE A 134 " pdb=" CG2 ILE A 134 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 1293 not shown) Planarity restraints: 1435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 102 " -0.015 2.00e-02 2.50e+03 1.39e-02 4.83e+00 pdb=" CG TRP H 102 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP H 102 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP H 102 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 102 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 102 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 102 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 102 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 102 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP H 102 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.033 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO H 109 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 59 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.25e+00 pdb=" N PRO L 60 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " -0.025 5.00e-02 4.00e+02 ... (remaining 1432 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1930 2.79 - 3.32: 7029 3.32 - 3.84: 13294 3.84 - 4.37: 14915 4.37 - 4.90: 26285 Nonbonded interactions: 63453 Sorted by model distance: nonbonded pdb=" OG SER A 168 " pdb=" O GLY A 307 " model vdw 2.260 2.440 nonbonded pdb=" O VAL A 83 " pdb=" OG1 THR A 87 " model vdw 2.316 2.440 nonbonded pdb=" OD2 ASP H 76 " pdb=" OG SER H 78 " model vdw 2.345 2.440 nonbonded pdb=" O ASP L 187 " pdb=" OH TYR L 194 " model vdw 2.350 2.440 nonbonded pdb=" O TRP H 111 " pdb=" OH TYR L 92 " model vdw 2.351 2.440 ... (remaining 63448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.030 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.030 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8413 Z= 0.230 Angle : 0.803 9.205 11444 Z= 0.432 Chirality : 0.048 0.243 1296 Planarity : 0.006 0.049 1435 Dihedral : 9.451 75.332 2970 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.21), residues: 1045 helix: -1.94 (0.20), residues: 374 sheet: -1.97 (0.29), residues: 262 loop : -2.61 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 102 HIS 0.008 0.002 HIS H 38 PHE 0.028 0.002 PHE A 103 TYR 0.026 0.002 TYR A 74 ARG 0.004 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A -68 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7694 (mtpp) REVERT: A -51 LYS cc_start: 0.8142 (tttt) cc_final: 0.7881 (mttt) REVERT: A -35 LEU cc_start: 0.7218 (tt) cc_final: 0.6988 (tt) REVERT: A -26 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6787 (mt-10) REVERT: A 41 ILE cc_start: 0.7252 (mt) cc_final: 0.6985 (mt) REVERT: A 42 ARG cc_start: 0.5848 (mtm110) cc_final: 0.5496 (ptp90) REVERT: A 61 ARG cc_start: 0.7687 (ttm110) cc_final: 0.7381 (ttp-110) REVERT: A 79 VAL cc_start: 0.8003 (m) cc_final: 0.7726 (t) REVERT: A 133 ARG cc_start: 0.7414 (mmt180) cc_final: 0.7138 (mmm160) REVERT: A 152 VAL cc_start: 0.7831 (t) cc_final: 0.7624 (p) REVERT: A 290 ILE cc_start: 0.7986 (mt) cc_final: 0.7491 (tt) REVERT: A 382 ILE cc_start: 0.8056 (mt) cc_final: 0.7674 (mt) REVERT: A 399 VAL cc_start: 0.6954 (t) cc_final: 0.6518 (p) REVERT: A 404 THR cc_start: 0.8137 (m) cc_final: 0.7670 (p) REVERT: A 408 THR cc_start: 0.8008 (m) cc_final: 0.7575 (p) REVERT: A 411 LYS cc_start: 0.7719 (ttpt) cc_final: 0.7396 (ttpt) REVERT: A 428 VAL cc_start: 0.7597 (p) cc_final: 0.6889 (t) REVERT: A 434 LEU cc_start: 0.7925 (tp) cc_final: 0.7711 (tp) REVERT: H 28 SER cc_start: 0.8035 (p) cc_final: 0.7764 (t) REVERT: H 130 THR cc_start: 0.7891 (p) cc_final: 0.7608 (t) REVERT: N 34 MET cc_start: 0.6133 (mtp) cc_final: 0.5913 (mtp) REVERT: N 89 GLU cc_start: 0.6957 (mp0) cc_final: 0.6222 (mp0) REVERT: L 43 LYS cc_start: 0.8732 (mttt) cc_final: 0.8479 (mtmm) REVERT: L 46 LYS cc_start: 0.8008 (mttm) cc_final: 0.7779 (mttm) REVERT: L 111 THR cc_start: 0.8670 (p) cc_final: 0.8426 (p) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2092 time to fit residues: 68.6926 Evaluate side-chains 204 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.0060 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.0770 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 0.1980 overall best weight: 0.2754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -42 GLN A 5 GLN A 172 GLN A 293 ASN A 386 GLN A 431 GLN H 42 GLN ** H 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 GLN L 39 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8413 Z= 0.167 Angle : 0.548 5.994 11444 Z= 0.282 Chirality : 0.041 0.156 1296 Planarity : 0.004 0.035 1435 Dihedral : 4.410 19.001 1153 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.24 % Allowed : 8.40 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.25), residues: 1045 helix: 0.05 (0.25), residues: 383 sheet: -1.18 (0.31), residues: 245 loop : -2.21 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 102 HIS 0.004 0.001 HIS A 27 PHE 0.012 0.001 PHE A 405 TYR 0.014 0.001 TYR L 50 ARG 0.002 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 212 time to evaluate : 0.867 Fit side-chains REVERT: A -68 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7745 (mtpp) REVERT: A -51 LYS cc_start: 0.8170 (tttt) cc_final: 0.7909 (mtmt) REVERT: A -26 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6860 (mt-10) REVERT: A 41 ILE cc_start: 0.7231 (mt) cc_final: 0.6962 (mt) REVERT: A 74 TYR cc_start: 0.7064 (m-10) cc_final: 0.6791 (m-10) REVERT: A 79 VAL cc_start: 0.7906 (m) cc_final: 0.7629 (t) REVERT: A 95 VAL cc_start: 0.7794 (p) cc_final: 0.7522 (t) REVERT: A 310 ASP cc_start: 0.6561 (t0) cc_final: 0.6095 (m-30) REVERT: A 346 GLN cc_start: 0.7590 (mt0) cc_final: 0.7298 (tt0) REVERT: A 404 THR cc_start: 0.8329 (m) cc_final: 0.7985 (p) REVERT: A 408 THR cc_start: 0.8229 (m) cc_final: 0.7815 (t) REVERT: A 434 LEU cc_start: 0.8009 (tp) cc_final: 0.7737 (tp) REVERT: H 24 SER cc_start: 0.8184 (m) cc_final: 0.7706 (t) REVERT: H 74 SER cc_start: 0.7453 (t) cc_final: 0.7051 (p) REVERT: H 116 TYR cc_start: 0.7486 (m-10) cc_final: 0.7193 (m-10) REVERT: H 177 VAL cc_start: 0.8396 (t) cc_final: 0.8072 (p) REVERT: N 83 MET cc_start: 0.5734 (ttm) cc_final: 0.5441 (ttm) REVERT: N 89 GLU cc_start: 0.6536 (mp0) cc_final: 0.6145 (mp0) REVERT: N 95 TYR cc_start: 0.7704 (m-10) cc_final: 0.7436 (m-80) REVERT: L 6 THR cc_start: 0.8550 (t) cc_final: 0.8119 (p) REVERT: L 43 LYS cc_start: 0.8769 (mttt) cc_final: 0.8515 (mtmm) REVERT: L 46 LYS cc_start: 0.8028 (mttm) cc_final: 0.7732 (mttm) outliers start: 20 outliers final: 9 residues processed: 223 average time/residue: 0.2085 time to fit residues: 62.5530 Evaluate side-chains 209 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 200 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 202 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 64 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 0.3980 chunk 94 optimal weight: 0.4980 chunk 102 optimal weight: 0.7980 chunk 84 optimal weight: 0.0050 chunk 93 optimal weight: 0.0770 chunk 32 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 overall best weight: 0.3152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -42 GLN A 172 GLN H 169 ASN L 149 GLN ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS L 212 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8413 Z= 0.181 Angle : 0.556 9.565 11444 Z= 0.280 Chirality : 0.041 0.129 1296 Planarity : 0.003 0.034 1435 Dihedral : 4.239 17.897 1153 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.69 % Allowed : 10.30 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.26), residues: 1045 helix: 0.86 (0.27), residues: 387 sheet: -0.76 (0.33), residues: 245 loop : -1.82 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 102 HIS 0.005 0.001 HIS A 27 PHE 0.012 0.001 PHE A -18 TYR 0.015 0.001 TYR L 92 ARG 0.004 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 215 time to evaluate : 0.944 Fit side-chains REVERT: A -68 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7718 (mtpp) REVERT: A -51 LYS cc_start: 0.8036 (tttt) cc_final: 0.7773 (mtmt) REVERT: A -26 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6881 (mt-10) REVERT: A -24 LYS cc_start: 0.7802 (mttt) cc_final: 0.7514 (mttp) REVERT: A 74 TYR cc_start: 0.7164 (m-10) cc_final: 0.6961 (m-10) REVERT: A 79 VAL cc_start: 0.7956 (m) cc_final: 0.7663 (t) REVERT: A 148 ARG cc_start: 0.6358 (mmm-85) cc_final: 0.6067 (mmm-85) REVERT: A 310 ASP cc_start: 0.6653 (t0) cc_final: 0.6354 (m-30) REVERT: A 373 ARG cc_start: 0.7344 (mmm160) cc_final: 0.7079 (ttm-80) REVERT: A 404 THR cc_start: 0.8260 (m) cc_final: 0.7951 (p) REVERT: A 408 THR cc_start: 0.8259 (m) cc_final: 0.7840 (t) REVERT: A 434 LEU cc_start: 0.8042 (tp) cc_final: 0.7811 (tp) REVERT: H 24 SER cc_start: 0.8389 (m) cc_final: 0.7884 (t) REVERT: H 74 SER cc_start: 0.7607 (t) cc_final: 0.7253 (p) REVERT: H 114 PHE cc_start: 0.8004 (m-80) cc_final: 0.7798 (m-10) REVERT: H 116 TYR cc_start: 0.7754 (m-10) cc_final: 0.7412 (m-10) REVERT: H 152 LEU cc_start: 0.7806 (tp) cc_final: 0.7539 (tp) REVERT: H 177 VAL cc_start: 0.8417 (t) cc_final: 0.8133 (p) REVERT: N 89 GLU cc_start: 0.6573 (mp0) cc_final: 0.6157 (mp0) REVERT: N 95 TYR cc_start: 0.7788 (m-10) cc_final: 0.7587 (m-80) REVERT: L 43 LYS cc_start: 0.8803 (mttt) cc_final: 0.8521 (mtmm) REVERT: L 46 LYS cc_start: 0.7976 (mttm) cc_final: 0.7712 (mttm) REVERT: L 142 TYR cc_start: 0.7737 (t80) cc_final: 0.7323 (t80) outliers start: 24 outliers final: 17 residues processed: 226 average time/residue: 0.2209 time to fit residues: 67.1260 Evaluate side-chains 212 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -34 GLU Chi-restraints excluded: chain A residue -29 ASP Chi-restraints excluded: chain A residue -16 ILE Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.0170 chunk 27 optimal weight: 0.9990 chunk 83 optimal weight: 0.0670 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8413 Z= 0.245 Angle : 0.597 9.256 11444 Z= 0.303 Chirality : 0.043 0.216 1296 Planarity : 0.003 0.030 1435 Dihedral : 4.364 18.780 1153 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.80 % Allowed : 12.88 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.27), residues: 1045 helix: 1.15 (0.27), residues: 387 sheet: -0.62 (0.34), residues: 245 loop : -1.70 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 102 HIS 0.005 0.001 HIS A 289 PHE 0.013 0.001 PHE L 141 TYR 0.013 0.002 TYR A 76 ARG 0.002 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 194 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A -51 LYS cc_start: 0.8104 (tttt) cc_final: 0.7710 (mttm) REVERT: A -26 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6853 (mt-10) REVERT: A -24 LYS cc_start: 0.7860 (mttt) cc_final: 0.7492 (mttp) REVERT: A 61 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.7473 (ttp-110) REVERT: A 79 VAL cc_start: 0.7975 (m) cc_final: 0.7619 (t) REVERT: A 116 VAL cc_start: 0.7810 (t) cc_final: 0.7572 (t) REVERT: A 148 ARG cc_start: 0.6436 (mmm-85) cc_final: 0.6231 (mmm-85) REVERT: A 162 LEU cc_start: 0.7797 (tp) cc_final: 0.7509 (tp) REVERT: A 310 ASP cc_start: 0.6798 (t0) cc_final: 0.6280 (m-30) REVERT: A 346 GLN cc_start: 0.7575 (mt0) cc_final: 0.7265 (tt0) REVERT: A 393 LYS cc_start: 0.7855 (mttt) cc_final: 0.7261 (mtmt) REVERT: A 404 THR cc_start: 0.8243 (m) cc_final: 0.7922 (p) REVERT: A 408 THR cc_start: 0.8349 (m) cc_final: 0.7874 (t) REVERT: A 434 LEU cc_start: 0.8069 (tp) cc_final: 0.7807 (tp) REVERT: H 24 SER cc_start: 0.8533 (m) cc_final: 0.8055 (t) REVERT: H 74 SER cc_start: 0.7791 (t) cc_final: 0.7461 (p) REVERT: H 90 ARG cc_start: 0.6897 (mtm110) cc_final: 0.6693 (mtp85) REVERT: H 114 PHE cc_start: 0.8192 (m-80) cc_final: 0.7883 (m-10) REVERT: H 152 LEU cc_start: 0.7681 (tp) cc_final: 0.7468 (tp) REVERT: H 177 VAL cc_start: 0.8490 (t) cc_final: 0.8243 (p) REVERT: N 89 GLU cc_start: 0.6735 (mp0) cc_final: 0.6241 (mp0) REVERT: L 6 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8093 (p) REVERT: L 46 LYS cc_start: 0.7957 (mttm) cc_final: 0.7660 (mttm) REVERT: L 118 PHE cc_start: 0.8175 (m-80) cc_final: 0.7969 (m-10) outliers start: 25 outliers final: 20 residues processed: 204 average time/residue: 0.2252 time to fit residues: 61.5727 Evaluate side-chains 212 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -29 ASP Chi-restraints excluded: chain A residue -16 ILE Chi-restraints excluded: chain A residue -9 ASP Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 74 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 90 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8413 Z= 0.209 Angle : 0.576 8.940 11444 Z= 0.290 Chirality : 0.042 0.236 1296 Planarity : 0.003 0.032 1435 Dihedral : 4.296 19.695 1153 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.91 % Allowed : 14.33 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.27), residues: 1045 helix: 1.35 (0.27), residues: 387 sheet: -0.46 (0.35), residues: 245 loop : -1.58 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 25 HIS 0.005 0.001 HIS A 27 PHE 0.024 0.001 PHE A 84 TYR 0.013 0.001 TYR L 142 ARG 0.002 0.000 ARG A 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 201 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: A -51 LYS cc_start: 0.8097 (tttt) cc_final: 0.7791 (mtmt) REVERT: A -26 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6847 (mt-10) REVERT: A -24 LYS cc_start: 0.7853 (mttt) cc_final: 0.7491 (mttp) REVERT: A -15 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8014 (tp) REVERT: A 27 HIS cc_start: 0.5499 (OUTLIER) cc_final: 0.4622 (m-70) REVERT: A 77 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7091 (mp) REVERT: A 79 VAL cc_start: 0.7912 (m) cc_final: 0.7574 (t) REVERT: A 95 VAL cc_start: 0.7816 (p) cc_final: 0.7511 (t) REVERT: A 148 ARG cc_start: 0.6439 (mmm-85) cc_final: 0.6236 (mmm-85) REVERT: A 149 TYR cc_start: 0.6427 (t80) cc_final: 0.6054 (t80) REVERT: A 162 LEU cc_start: 0.7814 (tp) cc_final: 0.7530 (tp) REVERT: A 204 LYS cc_start: 0.8414 (tttt) cc_final: 0.8195 (tttt) REVERT: A 310 ASP cc_start: 0.6797 (t0) cc_final: 0.6362 (m-30) REVERT: A 346 GLN cc_start: 0.7586 (mt0) cc_final: 0.7251 (tt0) REVERT: A 404 THR cc_start: 0.8206 (m) cc_final: 0.7923 (p) REVERT: A 408 THR cc_start: 0.8351 (m) cc_final: 0.7989 (t) REVERT: A 409 ILE cc_start: 0.7996 (mt) cc_final: 0.7716 (mt) REVERT: A 434 LEU cc_start: 0.8082 (tp) cc_final: 0.7822 (tp) REVERT: H 24 SER cc_start: 0.8508 (m) cc_final: 0.8025 (t) REVERT: H 74 SER cc_start: 0.7828 (t) cc_final: 0.7492 (p) REVERT: H 114 PHE cc_start: 0.8086 (m-80) cc_final: 0.7846 (m-10) REVERT: H 116 TYR cc_start: 0.8069 (m-10) cc_final: 0.7781 (m-80) REVERT: H 152 LEU cc_start: 0.7709 (tp) cc_final: 0.7448 (tp) REVERT: N 89 GLU cc_start: 0.6741 (mp0) cc_final: 0.6242 (mp0) REVERT: L 6 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8117 (p) REVERT: L 46 LYS cc_start: 0.7969 (mttm) cc_final: 0.7667 (mttm) outliers start: 26 outliers final: 20 residues processed: 212 average time/residue: 0.2139 time to fit residues: 60.6143 Evaluate side-chains 221 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 197 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -29 ASP Chi-restraints excluded: chain A residue -15 LEU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 103 PHE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.9111 > 50: distance: 47 - 68: 22.864 distance: 55 - 82: 31.626 distance: 60 - 90: 31.423 distance: 63 - 68: 24.197 distance: 64 - 98: 23.483 distance: 68 - 69: 22.885 distance: 69 - 70: 26.879 distance: 69 - 72: 19.372 distance: 70 - 71: 41.744 distance: 70 - 82: 59.252 distance: 71 - 106: 36.247 distance: 72 - 73: 12.864 distance: 73 - 74: 7.306 distance: 73 - 75: 15.147 distance: 74 - 76: 19.004 distance: 75 - 77: 16.481 distance: 75 - 78: 12.028 distance: 76 - 77: 9.691 distance: 77 - 79: 11.483 distance: 78 - 80: 10.374 distance: 79 - 81: 14.307 distance: 80 - 81: 25.732 distance: 82 - 83: 19.090 distance: 83 - 84: 22.797 distance: 83 - 86: 38.950 distance: 84 - 85: 22.319 distance: 84 - 90: 26.328 distance: 85 - 114: 8.535 distance: 86 - 87: 29.240 distance: 87 - 88: 24.050 distance: 87 - 89: 31.771 distance: 90 - 91: 35.337 distance: 91 - 92: 33.229 distance: 91 - 94: 19.816 distance: 92 - 93: 16.130 distance: 92 - 98: 46.174 distance: 95 - 96: 38.381 distance: 95 - 97: 43.651 distance: 98 - 99: 31.388 distance: 99 - 100: 29.151 distance: 99 - 102: 9.900 distance: 100 - 101: 44.646 distance: 100 - 106: 25.543 distance: 102 - 103: 31.401 distance: 103 - 104: 55.685 distance: 103 - 105: 15.990 distance: 106 - 107: 18.310 distance: 107 - 108: 32.130 distance: 107 - 110: 51.391 distance: 108 - 109: 26.759 distance: 108 - 114: 32.344 distance: 111 - 112: 14.768 distance: 111 - 113: 25.595 distance: 114 - 115: 15.615 distance: 115 - 116: 6.297 distance: 115 - 118: 28.920 distance: 116 - 117: 11.585 distance: 116 - 122: 20.036 distance: 118 - 119: 11.789 distance: 119 - 120: 5.735 distance: 119 - 121: 28.410 distance: 122 - 123: 12.382 distance: 123 - 124: 4.419 distance: 124 - 125: 41.487 distance: 124 - 126: 28.902 distance: 126 - 127: 14.024 distance: 127 - 128: 8.659 distance: 127 - 130: 8.065 distance: 128 - 129: 25.719 distance: 128 - 136: 22.550 distance: 130 - 131: 5.253 distance: 131 - 132: 20.111 distance: 131 - 133: 10.390 distance: 132 - 134: 8.448 distance: 133 - 135: 18.756 distance: 134 - 135: 13.213 distance: 136 - 137: 41.175 distance: 137 - 138: 22.911 distance: 137 - 140: 23.170 distance: 138 - 139: 30.627 distance: 138 - 142: 4.161 distance: 140 - 141: 40.938 distance: 142 - 143: 7.533 distance: 143 - 144: 19.291 distance: 144 - 145: 26.189 distance: 144 - 149: 14.787 distance: 145 - 172: 20.505 distance: 146 - 147: 22.173 distance: 146 - 148: 14.119